Advanced Workshop for SRA & dbGaP Users

Presented March 23, 2016. This webinar is for those who have experience with RNA-Seq analysis, variant calling or metagenomic data and want to work with large genomic datasets, use cloud computing for analyzing genomic datasets and perform parallel work on genomic datasets. You will learn how to call variants from SRA and dbGaP with GATK, realign reads with HISAT2, view expression levels and variants, search SRA data rapidly, integrate with Spark and mount dbGaP to an EBS volume.

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Categories

Archives

Archives

What is RNA-Seq?

long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. Sequencing adaptors (blue) are subsequently added to each cDNA fragment and a short sequence is obtained from each cDNA using high-throughput sequencing technology. The resulting sequence reads are aligned with the reference genome or transcriptome, and classified as three types: exonic reads, junction reads and poly(A) end-reads. These three types are used to generate a base-resolution expression profile for each gene. Nat Rev Genet 10(1):57-63 (2009)